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- PDB-1jli: HUMAN INTERLEUKIN 3 (IL-3) MUTANT WITH TRUNCATION AT BOTH N-AND C... -

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Basic information

Entry
Database: PDB / ID: 1jli
TitleHUMAN INTERLEUKIN 3 (IL-3) MUTANT WITH TRUNCATION AT BOTH N-AND C-TERMINI AND 14 RESIDUE CHANGES, NMR, MINIMIZED AVERAGE STRUCTURE
ComponentsINTERLEUKIN 3
KeywordsCYTOKINE / HEMATOPOIETIC GROWTH FACTOR / COLONY-STIMULATING FACTOR
Function / homology
Function and homology information


interleukin-3 receptor binding / RUNX1 regulates transcription of genes involved in interleukin signaling / interleukin-3-mediated signaling pathway / cell surface receptor signaling pathway via STAT / embryonic hemopoiesis / positive regulation of peptidyl-tyrosine phosphorylation / Interleukin-3, Interleukin-5 and GM-CSF signaling / Interleukin receptor SHC signaling / cytokine activity / growth factor activity ...interleukin-3 receptor binding / RUNX1 regulates transcription of genes involved in interleukin signaling / interleukin-3-mediated signaling pathway / cell surface receptor signaling pathway via STAT / embryonic hemopoiesis / positive regulation of peptidyl-tyrosine phosphorylation / Interleukin-3, Interleukin-5 and GM-CSF signaling / Interleukin receptor SHC signaling / cytokine activity / growth factor activity / nervous system development / cell-cell signaling / RAF/MAP kinase cascade / immune response / positive regulation of cell population proliferation / extracellular space / extracellular region
Similarity search - Function
Interleukin-3 / Interleukin-3 / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR
AuthorsFeng, Y. / Klein, B.K. / Mcwherter, C.A.
Citation
Journal: J.Mol.Biol. / Year: 1996
Title: Three-dimensional solution structure and backbone dynamics of a variant of human interleukin-3.
Authors: Feng, Y. / Klein, B.K. / McWherter, C.A.
#1: Journal: Biochemistry / Year: 1995
Title: 1H, 13C, and 15N NMR Resonance Assignments, Secondary Structure, and Backbone Topology of a Variant of Human Interleukin-3
Authors: Feng, Y. / Klein, B.K. / Vu, L. / Aykent, S. / Mcwherter, C.A.
History
DepositionDec 14, 1995Processing site: BNL
Revision 1.0Jun 16, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: INTERLEUKIN 3


Theoretical massNumber of molelcules
Total (without water)12,8451
Polymers12,8451
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
Representative

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Components

#1: Protein INTERLEUKIN 3 / MULTI-CSF


Mass: 12844.856 Da / Num. of mol.: 1
Mutation: DEL(1-13), V14A, N18I, T25H, Q29R, L32N, F37P, G42S, Q45M, N51R, R55T, E59L, N62V, S67H, Q69E, DEL(126-133)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PMON 13302 / Production host: Escherichia coli (E. coli) / Strain (production host): JM101 / References: UniProt: P08700
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Crystal grow
*PLUS
Method: other / Details: NMR

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR softwareName: X-PLOR / Version: 3.1 / Developer: BRUNGER / Classification: refinement
RefinementSoftware ordinal: 1
Details: AS IN X-PLOR PARALLHDG.PRO STRUCTURES WERE CALCULATED USING A SIMULATED ANNEALING PROTOCOL IN X-PLOR. INPUT CONSTRAINTS ARE AS FOLLOWS: 1659 NUCLEAR OVERHAUSER ENHANCEMENT (NOE) (799 INTRA- ...Details: AS IN X-PLOR PARALLHDG.PRO STRUCTURES WERE CALCULATED USING A SIMULATED ANNEALING PROTOCOL IN X-PLOR. INPUT CONSTRAINTS ARE AS FOLLOWS: 1659 NUCLEAR OVERHAUSER ENHANCEMENT (NOE) (799 INTRA-RESIDUE; 342 SEQUENTIAL (I-J =1); 236 MEDIUM-RANGE INTERRESIDUE (<1 I-J <=5); 282 LONG-RANGE INTERRESIDUE (I-J >5)); 38 PAIRS OF HYDROGEN-BOND RESTRAINTS; 76 PHI TORSION ANGLE RESTRAINTS. PSEUDOATOM POSITIONS WERE USED FOR CONSTRAINTS INVOLVING METHYLENE, AROMATIC, AND METHYL PROTONS. THE COORDINATES DEPOSITED HERE ARE OBTAINED BY AVERAGING 25 CONVERGED STRUCTURES PRIOR TO A RESTRAINED ENERGY MINIMIZATION. A COMPARISON OF THE FAMILY OF THE 25 STRUCTURES WITH THE AVERAGED STRUCTURE GIVES RMSD VALUES OF 0.88 ANGSTROMS FOR ALL (N,CA,C') EXCEPT RESIDUES 28 - 39, AND 0.41 ANGSTROMS FOR (N,CA,C') OF HELICAL REGIONS (RESIDUES 16 - 26, 42 - 49, 54 - 67, 72 - 84, AND 104 - 122).
NMR ensembleConformers submitted total number: 1

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